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- PDB-3vac: Crystal Structure of the CFA/I Enterotoxigenic E. coli adhesin Cf... -

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Basic information

Entry
Database: PDB / ID: 3vac
TitleCrystal Structure of the CFA/I Enterotoxigenic E. coli adhesin CfaE mutant G168D
ComponentsCFA/I fimbrial subunit E
KeywordsCELL ADHESION / Ig fold / CFA/I ETEC adhesin
Function / homology
Function and homology information


CFA/I fimbrial subunit E, adhesin domain / CblD-like pilus biogenesis initiator / CFA/I fimbrial subunit E, adhesin domain / CblD like pilus biogenesis initiator / CFA/I fimbrial subunit E, pilin domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CFA/I fimbrial subunit E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsLiu, Y. / Esser, L. / Xia, D.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Tight Conformational Coupling between the Domains of the Enterotoxigenic Escherichia coli Fimbrial Adhesin CfaE Regulates Binding State Transition.
Authors: Liu, Y. / Esser, L. / Interlandi, G. / Kisiela, D.I. / Tchesnokova, V. / Thomas, W.E. / Sokurenko, E. / Xia, D. / Savarino, S.J.
History
DepositionDec 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CFA/I fimbrial subunit E
B: CFA/I fimbrial subunit E


Theoretical massNumber of molelcules
Total (without water)78,7862
Polymers78,7862
Non-polymers00
Water4,486249
1
A: CFA/I fimbrial subunit E


Theoretical massNumber of molelcules
Total (without water)39,3931
Polymers39,3931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CFA/I fimbrial subunit E


Theoretical massNumber of molelcules
Total (without water)39,3931
Polymers39,3931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.066, 126.364, 78.701
Angle α, β, γ (deg.)90.000, 100.490, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A23 - 200
2111B23 - 200
1121A201 - 378
2121B201 - 378

NCS ensembles :
ID
1
2

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Components

#1: Protein CFA/I fimbrial subunit E / dscCfaE / Colonization factor antigen I subunit E


Mass: 39393.168 Da / Num. of mol.: 2 / Fragment: UNP residues 23-360 / Mutation: G168D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cfaE / Production host: Escherichia coli (E. coli) / References: UniProt: P25734
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.91 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1 M sodium citrate, pH 5.8, 1.5 M sodium chloride, 18% PEG4000, 50 mM guanidine chloride, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationMonochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 33308 / % possible obs: 95.3 % / Rmerge(I) obs: 0.098

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0066refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→46.777 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.899 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 20.889 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.497 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1498 4.9 %RANDOM
Rwork0.1836 ---
all0.194 ---
obs0.1861 30301 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 119.59 Å2 / Biso mean: 56.054 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å2-1.78 Å2
2--1.4 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5536 0 0 249 5785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225649
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.967676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8835710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.21825.276254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.01715966
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7281526
X-RAY DIFFRACTIONr_chiral_restr0.0930.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214276
X-RAY DIFFRACTIONr_mcbond_it1.121.53544
X-RAY DIFFRACTIONr_mcangle_it2.09325742
X-RAY DIFFRACTIONr_scbond_it2.42632105
X-RAY DIFFRACTIONr_scangle_it4.0394.51934
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11382TIGHT POSITIONAL0.10.05
11382TIGHT THERMAL0.190.5
21386TIGHT POSITIONAL0.040.05
21386TIGHT THERMAL0.090.5
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 110 -
Rwork0.268 1889 -
all-1999 -
obs--87.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.37750.20231.45630.17190.1051.9883-0.00390.00360.0977-0.0875-0.08970.00380.05230.10220.09370.06990.03120.00710.10860.03070.042539.4794-0.294760.667
22.70740.97280.03474.01891.57662.8483-0.1486-0.0949-0.0804-0.1439-0.30960.60490.5239-0.47670.45820.255-0.1118-0.01520.0927-0.05910.15655.4435-21.696931.0615
30.85760.16890.70480.48010.70182.64920.02820.22880.03440.05530.0459-0.04250.023-0.0851-0.0740.01450.0112-0.0130.14370.02040.04714.04320.71269.0622
41.10920.4542-0.90743.09381.95584.11820.16530.01170.19360.4988-0.18470.1204-0.155-0.27380.01940.24380.0317-0.02650.0344-0.02360.05915.048421.325654.7623
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 200
2X-RAY DIFFRACTION2A201 - 378
3X-RAY DIFFRACTION3B23 - 200
4X-RAY DIFFRACTION4B201 - 378

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